Carl, sorry about the long delay in responding. FLAC is also my preferred format, without question. I generally only convert DTS files to FLAC if I don't have a lossless source available. Doing listening tests between DTS surround files and their MLP versions confirms that DTS sounds noticeably worse, at least through headphones. Mostly I don't buy discs that only offer DTS unless there are no other versions available. I tend to like surround albums so will put up with DTS if it's the only way to get that. For some reason, OCD? I will always rip most of the native formats from the discs I buy to my PC, including the raw DTS files. The only exception I make is AC3, they're just not worth bothering with. So anyway, a while back I was investigating DTS tagging and found little useful info except that some people had encapsulated the raw DTS WAVs into FLAC allowing them to be tagged.
I was surprised when JRiver seemed to offer extensive tagging support for the undecoded DTS files. It's a shame nobody can confirm how it's doing this?
In response to your question. I too have done my share of head-scratching about ripping DTS using DVD-Audio Extractor, you might find some of what I've learned helpful: Yes - when I last tried, DTS files could only be ripped to FLAC at up to 48Khz which matches the sample rate of the encoded DTS file which is not necessarily the same thing as the undecoded audio sample rate. When I asked DVD-AE they confirmed this limitation but they had plans to raise it to 96Khz in the future.
I only have a smaller selection of true DTS 96/24 files and when you bitstream them to your AV Amp they should identify this on the display. To rip these in true 96Khz you need to extract the raw DTS files using DVD-AE then use a tool like eac3to for FLAC conversion. I found one that has a GUI which is easier to use ('eac3to and more GUI'). eac3to is great to learn as you can also use it to rip Dolby TrueHD and DTS-HD. These seem to be the new formats coming to us on Blu-Ray Pure Audio discs.
When I look back at all the different types of HD audio disks I've bought and had to work out how to rip, it never ceases to amaze me. When will these companies settle on a stable standard? /me glances down at the PS3 I bought so I could backup my SACDs. By the way JRiver does a brilliant job of managing and playing decrypted SACD ISOs. You can play DSD back at crazy bitrates of 352Khz if you have the hardware. Even puts FLAC in the shade.
Paul